GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ybhL in Pseudovibrio axinellae Ad2

Align The YbhL (AceP) protein. Possibly a pmf-dependent acetate uptake transporter. [14C]Acetate uptake was inhibited by CCCP as well as cold acetate, serine, α-ketoglutarate, lactate, and succinate (M. Inouye, personal communication) (characterized)
to candidate WP_068008058.1 PsAD2_RS15965 Bax inhibitor-1/YccA family protein

Query= TCDB::P0AAC4
         (234 letters)



>NCBI__GCF_001623255.1:WP_068008058.1
          Length = 261

 Score =  201 bits (511), Expect = 1e-56
 Identities = 110/238 (46%), Positives = 157/238 (65%), Gaps = 22/238 (9%)

Query: 15  AGLQTYMAQVYGWMTVGLLLTAFVAWYAANSAAVME-------------------LLFTN 55
           AGL+ YM +VY +M VG+ +T  +A   + +A   +                   +L+T+
Sbjct: 26  AGLRAYMLRVYNYMAVGVAITGVLALLTSMAATTTDSSMAAAQLGNGDYLTNLGVMLYTS 85

Query: 56  RVFLIGLIIAQLALVIVLSAMIQKLSAGVTTMLFMLYSALTGLTLSSIFIVYTAASIAST 115
            +  + +++A L  V  LSA I K+SA    M F  ++AL G++LSSIF+VYT  SIA  
Sbjct: 86  PLRWV-VMLAPLGFVFFLSARISKMSASAAQMTFWAFAALMGVSLSSIFLVYTGNSIARV 144

Query: 116 FVVTAGMFGAMSLYGYTTKRDLSGFGNMLFMALIGIVLASLVNFWLKSEALMWAVTYIGV 175
           F ++A  FGA+SL+GYTTK+DLS +G+ LFM LIGI++AS+VN +L S AL +A++ +GV
Sbjct: 145 FFISAASFGALSLFGYTTKKDLSAWGSFLFMGLIGIIIASVVNLFLGSSALQFAISVVGV 204

Query: 176 IVFVGLTAYDTQKLKNMGEQIDTRDTSNLRKYSILGALTLYLDFINLFLMLLRIFGNR 233
           +VF GLTAYDTQ++K M   +D  D+    K +I+GAL LYLDFINLF+MLL +FGNR
Sbjct: 205 LVFAGLTAYDTQQIKEMYAAVD--DSEVAGKKAIMGALRLYLDFINLFIMLLSLFGNR 260


Lambda     K      H
   0.330    0.140    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 232
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 234
Length of database: 261
Length adjustment: 24
Effective length of query: 210
Effective length of database: 237
Effective search space:    49770
Effective search space used:    49770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory